What Is "obabel" Command

Cheminformatics Tutorials - Herong's Tutorial Examples

∟What Is "obabel" Command

This section provides a quick introduction on the 'obabel' command, which reads molecule information in any given format, processes it and generates output in any given format.

What Is "obabel" Command? - "obabel" is the command to invoke Open Babel to read molecule information in any given format, process it and generate output in any given format.

Note that new releases use "obabel" command instead of "babel". And its command line syntax has some small changes too. So you may need to revise your automated scripts accordingly, if you are migrating from Open Babel old releases.

To access the "obabel" command, you have to know the absolute path of the "obabel" program file, which is different depending on your Open Babel installations. Here are some examples:

# - Anaconda installation on Linux:
herong$ /usr/local/anaconda3/envs/openbabel/bin/obabel -V
  Open Babel 3.1.0 -- Aug 18 2019 -- 08:52:33

# - Binary package installation on Windows:
herong> "C:\Program Files\OpenBabel-3.1.1\obabel" -V
  Open Babel 3.1.1 -- May 16 2020 -- 11:57:55

# - Source code installation on Linux:
herong$ /usr/local/bin/obabel -V
  Open Babel 3.1.0 -- Jul 19 2019 -- 10:30:02

# - Binary package installation on macOS:
herong$ /usr/local/bin/obabel -V
  Open Babel 2.3.1 -- Oct 13 2011 -- 15:14:48

To avoid typing the full path of the "obabel" command, you can put the path name into the PATH environment variable. Here is how to do it on a Linux system.

herong$ export PATH=/usr/local/anaconda3/envs/openbabel/bin/:$PATH

herong$ obabel -V
  Open Babel 3.1.0 -- Aug 18 2019 -- 08:52:33

Now you can start learning "obabel" command by running the help command as shown below:

herong$ obabel -H

Open Babel converts chemical structures from one file format to another

Usage:
obabel [-i<input-type>] <infilename> [-o<output-type>] \
  -O<outfilename> [Options]

The extension of a file decides the format, unless it is overridden
 by -i or -o options, e.g. -icml, or -o smi
See below for available format-types, which are the same as the
file extensions and are case independent.
If no input or output file is given stdin or stdout are used instead.

More than one input file can be specified and their names can contain
wildcard chars (* and ?). The format of each file can be different unless
the -i option has been used, when they are all the same.
By default, the molecules are aggregated in the output file,
 but see -m option, Splitting, below.

Options, other than -i -o -O -m, must come after the input files.

Conversion options
-f <#> Start import at molecule # specified
-l <#> End import at molecule # specified
-e Continue with next object after error, if possible
-z Compress the output with gzip
-zin Decompress the input with gzip
-k Attempt to translate keywords
-H Outputs this help text
-Hfff (fff is file format ID e.g. -Hcml) gives format info
-Hall Outputs details of all formats
-V Outputs version number
-L <category> Lists plugin classes of this category, e.g. <formats>
   Use just -L for a list of plugin categories.
   Use -L <ID> e.g. -L sdf for details of a format or other plugin.
-m Produces multiple output files, to allow:
    Splitting: e.g.        obabel infile.mol -O new.smi -m
      puts each molecule into new1.smi new2.smi etc
    Batch conversion: e.g. obabel *.mol -osmi -m
      converts each input file to a .smi file
Interface to OBAPI internals
API options, e.g. ---errorlevel 2
 errorlevel # min warning level displayed

To see a list of recognized file formats use
  babel -L formats [read] [write]
To see details and specific options for a particular format, e.g CML, use
  babel -L cml